.TH g_select 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_select - selects groups of atoms based on flexible textual selections

.B VERSION 4.5
.SH SYNOPSIS
\f3g_select\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-sf" " selection.dat "
.BI "\-n" " index.ndx "
.BI "\-os" " size.xvg "
.BI "\-oc" " cfrac.xvg "
.BI "\-oi" " index.dat "
.BI "\-om" " mask.dat "
.BI "\-on" " index.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-xvg" " enum "
.BI "\-[no]rmpbc" ""
.BI "\-[no]pbc" ""
.BI "\-select" " string "
.BI "\-selrpos" " enum "
.BI "\-seltype" " enum "
.BI "\-[no]dump" ""
.BI "\-[no]norm" ""
.BI "\-[no]cfnorm" ""
.BI "\-resnr" " enum "
.SH DESCRIPTION
\&g_select writes out basic data about dynamic selections.
\&It can be used for some simple analyses, or the output can
\&be combined with output from other programs and/or external
\&analysis programs to calculate more complex things.
\&Any combination of the output options is possible, but note
\&that \fB \-om\fR only operates on the first selection.


\&With \fB \-os\fR, calculates the number of positions in each
\&selection for each frame. With \fB \-norm\fR, the output is
\&between 0 and 1 and describes the fraction from the maximum
\&number of positions (e.g., for selection 'resname RA and x  5'
\&the maximum number of positions is the number of atoms in
\&RA residues). With \fB \-cfnorm\fR, the output is divided
\&by the fraction covered by the selection.
\&\fB \-norm\fR and \fB \-cfnorm\fR can be specified independently
\&of one another.


\&With \fB \-oc\fR, the fraction covered by each selection is
\&written out as a function of time.


\&With \fB \-oi\fR, the selected atoms/residues/molecules are
\&written out as a function of time. In the output, the first
\&column contains the frame time, the second contains the number
\&of positions, followed by the atom/residue/molecule numbers.
\&If more than one selection is specified, the size of the second
\&group immediately follows the last number of the first group
\&and so on. With \fB \-dump\fR, the frame time and the number
\&of positions is omitted from the output. In this case, only one
\&selection can be given.


\&With \fB \-on\fR, the selected atoms are written as a index file
\&compatible with make_ndx and the analyzing tools. Each selection
\&is written as a selection group and for dynamic selections a
\&group is written for each frame.


\&For residue numbers, the output of \fB \-oi\fR can be controlled
\&with \fB \-resnr\fR: \fB number\fR (default) prints the residue
\&numbers as they appear in the input file, while \fB index\fR prints
\&unique numbers assigned to the residues in the order they appear
\&in the input file, starting with 1. The former is more intuitive,
\&but if the input contains multiple residues with the same number,
\&the output can be less useful.


\&With \fB \-om\fR, a mask is printed for the first selection
\&as a function of time. Each line in the output corresponds to
\&one frame, and contains either 0/1 for each atom/residue/molecule
\&possibly selected. 1 stands for the atom/residue/molecule being
\&selected for the current frame, 0 for not selected.
\&With \fB \-dump\fR, the frame time is omitted from the output.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-sf" " selection.dat" 
.B Input, Opt.
 Generic data file 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-os" " size.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oc" " cfrac.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oi" " index.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-om" " mask.dat" 
.B Output, Opt.
 Generic data file 

.BI "\-on" " index.ndx" 
.B Output, Opt.
 Index file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]rmpbc"  "yes   "
 Make molecules whole for each frame

.BI "\-[no]pbc"  "yes   "
 Use periodic boundary conditions for distance calculation

.BI "\-select"  " string" " " 
 Selection string (use 'help' for help)

.BI "\-selrpos"  " enum" " atom" 
 Selection reference position: \fB atom\fR, \fB res_com\fR, \fB res_cog\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB whole_res_com\fR, \fB whole_res_cog\fR, \fB whole_mol_com\fR, \fB whole_mol_cog\fR, \fB part_res_com\fR, \fB part_res_cog\fR, \fB part_mol_com\fR, \fB part_mol_cog\fR, \fB dyn_res_com\fR, \fB dyn_res_cog\fR, \fB dyn_mol_com\fR or \fB dyn_mol_cog\fR

.BI "\-seltype"  " enum" " atom" 
 Default analysis positions: \fB atom\fR, \fB res_com\fR, \fB res_cog\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB whole_res_com\fR, \fB whole_res_cog\fR, \fB whole_mol_com\fR, \fB whole_mol_cog\fR, \fB part_res_com\fR, \fB part_res_cog\fR, \fB part_mol_com\fR, \fB part_mol_cog\fR, \fB dyn_res_com\fR, \fB dyn_res_cog\fR, \fB dyn_mol_com\fR or \fB dyn_mol_cog\fR

.BI "\-[no]dump"  "no    "
 Do not print the frame time (\-om, \-oi) or the index size (\-oi)

.BI "\-[no]norm"  "no    "
 Normalize by total number of positions with \-os

.BI "\-[no]cfnorm"  "no    "
 Normalize by covered fraction with \-os

.BI "\-resnr"  " enum" " number" 
 Residue number output type: \fB number\fR or \fB index\fR

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
